---
_id: '9741'
abstract:
- lang: eng
text: In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments.
article_processing_charge: No
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: 'Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. 2014.
doi:10.5061/dryad.85dn7'
apa: 'Lagator, M., Colegrave, N., & Neve, P. (2014). Data from: Selection history
and epistatic interactions impact dynamics of adaptation to novel environmental
stresses. Dryad. https://doi.org/10.5061/dryad.85dn7'
chicago: 'Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History
and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental
Stresses.” Dryad, 2014. https://doi.org/10.5061/dryad.85dn7.'
ieee: 'M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and
epistatic interactions impact dynamics of adaptation to novel environmental stresses.”
Dryad, 2014.'
ista: 'Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses, Dryad,
10.5061/dryad.85dn7.'
mla: 'Lagator, Mato, et al. Data from: Selection History and Epistatic Interactions
Impact Dynamics of Adaptation to Novel Environmental Stresses. Dryad, 2014,
doi:10.5061/dryad.85dn7.'
short: M. Lagator, N. Colegrave, P. Neve, (2014).
date_created: 2021-07-28T08:48:06Z
date_published: 2014-08-21T00:00:00Z
date_updated: 2026-08-12T06:26:09Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.85dn7
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.85dn7
month: '08'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2036'
relation: used_in_publication
status: public
status: public
title: 'Data from: Selection history and epistatic interactions impact dynamics of
adaptation to novel environmental stresses'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2014'
...
---
_id: '2251'
abstract:
- lang: eng
text: 'Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated
to be involved in memory consolidation. However, more recent work has investigated
SWRs that occur during active waking behaviour: findings that suggest that SWRs
may also play a role in cell assembly strengthening or spatial working memory.
Do such theories of SWR function apply to animal learning? This review discusses
how general theories linking SWRs to memory-related function may explain circuit
mechanisms related to rodent spatial learning and to the associated stabilization
of new cognitive maps.'
article_number: '20120528'
article_processing_charge: No
author:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: David
full_name: Dupret, David
last_name: Dupret
citation:
ama: Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London
Series B, Biological Sciences. 2014;369(1635). doi:10.1098/rstb.2012.0528
apa: Csicsvari, J. L., & Dupret, D. (2014). Sharp wave/ripple network oscillations
and learning-associated hippocampal maps. Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2012.0528
chicago: Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society, 2014.
https://doi.org/10.1098/rstb.2012.0528.
ieee: J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and
learning-associated hippocampal maps,” Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences, vol. 369, no. 1635. Royal
Society, 2014.
ista: Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences. 369(1635), 20120528.
mla: Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635,
20120528, Royal Society, 2014, doi:10.1098/rstb.2012.0528.
short: J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences 369 (2014).
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T11:56:34Z
date_published: 2014-02-05T00:00:00Z
date_updated: 2026-08-12T06:27:15Z
day: '05'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1098/rstb.2012.0528
external_id:
isi:
- '000332465300014'
pmid:
- '24366138'
file:
- access_level: open_access
checksum: 51beb33de71c9c19e0c205a20d206f9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:24Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5006'
file_name: IST-2016-527-v1+1_20120528.full.pdf
file_size: 771896
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 369'
isi: 1
issue: '1635'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
issn:
- 0962-8436
publication_status: published
publisher: Royal Society
publist_id: '4697'
pubrep_id: '527'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sharp wave/ripple network oscillations and learning-associated hippocampal
maps
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 369
year: '2014'
...
---
_id: '1821'
abstract:
- lang: eng
text: We review recent progress towards a rigorous understanding of the Bogoliubov
approximation for bosonic quantum many-body systems. We focus, in particular,
on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A
list of open problems will be discussed at the end.
article_number: '1.4881536'
article_processing_charge: No
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation.
Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536
apa: Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4881536
chicago: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics. AIP Publishing, 2014.
https://doi.org/10.1063/1.4881536.
ieee: R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation,” Journal of Mathematical Physics, vol. 55, no. 7. AIP Publishing,
2014.
ista: Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov
approximation. Journal of Mathematical Physics. 55(7), 1.4881536.
mla: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov
Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536,
AIP Publishing, 2014, doi:10.1063/1.4881536.
short: R. Seiringer, Journal of Mathematical Physics 55 (2014).
corr_author: '1'
date_created: 2018-12-11T11:54:11Z
date_published: 2014-06-26T00:00:00Z
date_updated: 2026-08-12T13:58:01Z
day: '26'
ddc:
- '510'
- '530'
department:
- _id: RoSe
doi: 10.1063/1.4881536
external_id:
isi:
- '000341174600010'
file:
- access_level: open_access
checksum: ed0efc93c10f1341155f0316af617b82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:49Z
date_updated: 2020-07-14T12:45:17Z
file_id: '5172'
file_name: IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf
file_size: 269171
relation: main_file
file_date_updated: 2020-07-14T12:45:17Z
has_accepted_license: '1'
intvolume: ' 55'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Journal of Mathematical Physics
publication_status: published
publisher: AIP Publishing
publist_id: '5285'
pubrep_id: '532'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '1822'
article_number: '075101'
article_processing_charge: No
author:
- first_name: Vojkan
full_name: Jakšić, Vojkan
last_name: Jakšić
- first_name: Claude
full_name: Pillet, Claude
last_name: Pillet
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics.
2014;55(7). doi:10.1063/1.4884877
apa: Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal
of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4884877
chicago: Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal
of Mathematical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4884877.
ieee: V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical
Physics, vol. 55, no. 7. AIP Publishing, 2014.
ista: Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical
Physics. 55(7), 075101.
mla: Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics,
vol. 55, no. 7, 075101, AIP Publishing, 2014, doi:10.1063/1.4884877.
short: V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).
date_created: 2018-12-11T11:54:12Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2026-08-12T13:58:20Z
day: '01'
department:
- _id: RoSe
doi: 10.1063/1.4884877
external_id:
isi:
- '000341174600001'
intvolume: ' 55'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
publication: Journal of Mathematical Physics
publication_status: published
publisher: AIP Publishing
publist_id: '5284'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introduction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
OA_type: closed access
_id: '22435'
abstract:
- lang: eng
text: Regions of vegetation transitions (ecotones) are known to be highly sensitive
to climate fluctuations. In this study, the Cellular-Automata Tree Grass Shrub
Simulator (CATGraSS) has been modified, calibrated and used with downscaled future
climate scenarios to examine the role of climate change on vegetation patterns
in a steep mountainous catchment (1.3 km2) located in Sicily, Italy. In the catchment,
north-facing slopes are mostly covered by trees and grass, and south-facing slopes
by Indian Fig opuntia and grass, with grasses dominating as elevation grows. CATGraSS
simulates solar radiation, evapotranspiration, and soil moisture in space and
time. Each model cell can hold a single plant type or can be bare soil. Plant
competition is modeled explicitly through mortality and the establishment of individual
plants in open spaces. In this study, CATGraSS is modified to account for heterogeneity
in soil thickness and tested in the study catchment using the historical climate
of the region. Predicted vegetation patterns are compared with those obtained
from satellite images. Results of model under current climate underscore the importance
of solar irradiance and soil thickness, especially in the uplands where soil is
shallow, in determining vegetation composition over complex terrain. A stochastic
weather generator is used to generate future climate change scenarios for the
catchment by downscaling GCM realizations in space and time. Future increase in
atmospheric CO2 concentration was considered through modifying the vegetation
water use efficiency and stomatal resistance for our study site. Model results
suggest that vegetation pattern is highly sensitive to temperature and rainfall
variations provided by climate scenarios (30% reduction of the annual precipitation
and a 2.8 °C increase of the mean annual temperature). Future climate change is
predicted to bring a considerable reorganization of the plant composition following
topographic patterns, leading to a decrease of trees cover at the expenses of
a grass expansion, which will cause loss of landscape vegetation diversity.
article_processing_charge: No
article_type: original
author:
- first_name: Domenico
full_name: Caracciolo, Domenico
last_name: Caracciolo
- first_name: Leonardo Valerio
full_name: Noto, Leonardo Valerio
last_name: Noto
- first_name: Erkan
full_name: Istanbulluoglu, Erkan
last_name: Istanbulluoglu
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Xiaochi
full_name: Zhou, Xiaochi
last_name: Zhou
citation:
ama: 'Caracciolo D, Noto LV, Istanbulluoglu E, Fatichi S, Zhou X. Climate change
and Ecotone boundaries: Insights from a cellular automata ecohydrology model in
a Mediterranean catchment with topography controlled vegetation patterns. Advances
in Water Resources. 2014;73:159-175. doi:10.1016/j.advwatres.2014.08.001'
apa: 'Caracciolo, D., Noto, L. V., Istanbulluoglu, E., Fatichi, S., & Zhou,
X. (2014). Climate change and Ecotone boundaries: Insights from a cellular automata
ecohydrology model in a Mediterranean catchment with topography controlled vegetation
patterns. Advances in Water Resources. Elsevier. https://doi.org/10.1016/j.advwatres.2014.08.001'
chicago: 'Caracciolo, Domenico, Leonardo Valerio Noto, Erkan Istanbulluoglu, Simone
Fatichi, and Xiaochi Zhou. “Climate Change and Ecotone Boundaries: Insights from
a Cellular Automata Ecohydrology Model in a Mediterranean Catchment with Topography
Controlled Vegetation Patterns.” Advances in Water Resources. Elsevier,
2014. https://doi.org/10.1016/j.advwatres.2014.08.001.'
ieee: 'D. Caracciolo, L. V. Noto, E. Istanbulluoglu, S. Fatichi, and X. Zhou, “Climate
change and Ecotone boundaries: Insights from a cellular automata ecohydrology
model in a Mediterranean catchment with topography controlled vegetation patterns,”
Advances in Water Resources, vol. 73. Elsevier, pp. 159–175, 2014.'
ista: 'Caracciolo D, Noto LV, Istanbulluoglu E, Fatichi S, Zhou X. 2014. Climate
change and Ecotone boundaries: Insights from a cellular automata ecohydrology
model in a Mediterranean catchment with topography controlled vegetation patterns.
Advances in Water Resources. 73, 159–175.'
mla: 'Caracciolo, Domenico, et al. “Climate Change and Ecotone Boundaries: Insights
from a Cellular Automata Ecohydrology Model in a Mediterranean Catchment with
Topography Controlled Vegetation Patterns.” Advances in Water Resources,
vol. 73, Elsevier, 2014, pp. 159–75, doi:10.1016/j.advwatres.2014.08.001.'
short: D. Caracciolo, L.V. Noto, E. Istanbulluoglu, S. Fatichi, X. Zhou, Advances
in Water Resources 73 (2014) 159–175.
das_tickbox: '1'
date_created: 2026-07-27T12:30:23Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2026-08-12T14:11:56Z
day: '01'
doi: 10.1016/j.advwatres.2014.08.001
extern: '1'
intvolume: ' 73'
keyword:
- CA model
- Climate change
- Ecohydrology
- Topography
language:
- iso: eng
month: '11'
oa_version: None
page: 159-175
publication: Advances in Water Resources
publication_identifier:
issn:
- 0309-1708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Climate change and Ecotone boundaries: Insights from a cellular automata ecohydrology
model in a Mediterranean catchment with topography controlled vegetation patterns'
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 73
year: '2014'
...
---
OA_type: closed access
_id: '22459'
abstract:
- lang: eng
text: Projections of climate change effects in streamflow are increasingly required
to plan water management strategies. These projections are however largely uncertain
due to the spread among climate model realizations, internal climate variability,
and difficulties in transferring climate model results at the spatial and temporal
scales required by catchment hydrology. A combination of a stochastic downscaling
methodology and distributed hydrological modeling was used in the ACQWA project
to provide projections of future streamflow (up to year 2050) for the upper Po
and Rhone basins, respectively located in northern Italy and south-western Switzerland.
Results suggest that internal (stochastic) climate variability is a fundamental
source of uncertainty, typically comparable or larger than the projected climate
change signal. Therefore, climate change effects in streamflow mean, frequency,
and seasonality can be masked by natural climatic fluctuations in large parts
of the analyzed regions. An exception to the overwhelming role of stochastic variability
is represented by high elevation catchments fed by glaciers where streamflow is
expected to be considerably reduced due to glacier retreat, with consequences
appreciable in the main downstream rivers in August and September. Simulations
also identify regions (west upper Rhone and Toce, Ticino river basins) where a
strong precipitation increase in the February to April period projects streamflow
beyond the range of natural climate variability during the melting season. This
study emphasizes the importance of including internal climate variability in climate
change analyses, especially when compared to the limited uncertainty that would
be accounted for by few deterministic projections. The presented results could
be useful in guiding more specific impact studies, although design or management
decisions should be better based on reliability and vulnerability criteria as
suggested by recent literature.
article_processing_charge: No
article_type: original
author:
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: S.
full_name: Rimkus, S.
last_name: Rimkus
- first_name: P.
full_name: Burlando, P.
last_name: Burlando
- first_name: R.
full_name: Bordoy, R.
last_name: Bordoy
citation:
ama: Fatichi S, Rimkus S, Burlando P, Bordoy R. Does internal climate variability
overwhelm climate change signals in streamflow? The upper Po and Rhone basin case
studies. Science of The Total Environment. 2014;493:1171-1182. doi:10.1016/j.scitotenv.2013.12.014
apa: Fatichi, S., Rimkus, S., Burlando, P., & Bordoy, R. (2014). Does internal
climate variability overwhelm climate change signals in streamflow? The upper
Po and Rhone basin case studies. Science of The Total Environment. Elsevier.
https://doi.org/10.1016/j.scitotenv.2013.12.014
chicago: Fatichi, Simone, S. Rimkus, P. Burlando, and R. Bordoy. “Does Internal
Climate Variability Overwhelm Climate Change Signals in Streamflow? The Upper
Po and Rhone Basin Case Studies.” Science of The Total Environment. Elsevier,
2014. https://doi.org/10.1016/j.scitotenv.2013.12.014.
ieee: S. Fatichi, S. Rimkus, P. Burlando, and R. Bordoy, “Does internal climate
variability overwhelm climate change signals in streamflow? The upper Po and Rhone
basin case studies,” Science of The Total Environment, vol. 493. Elsevier,
pp. 1171–1182, 2014.
ista: Fatichi S, Rimkus S, Burlando P, Bordoy R. 2014. Does internal climate variability
overwhelm climate change signals in streamflow? The upper Po and Rhone basin case
studies. Science of The Total Environment. 493, 1171–1182.
mla: Fatichi, Simone, et al. “Does Internal Climate Variability Overwhelm Climate
Change Signals in Streamflow? The Upper Po and Rhone Basin Case Studies.” Science
of The Total Environment, vol. 493, Elsevier, 2014, pp. 1171–82, doi:10.1016/j.scitotenv.2013.12.014.
short: S. Fatichi, S. Rimkus, P. Burlando, R. Bordoy, Science of The Total Environment
493 (2014) 1171–1182.
das_tickbox: '1'
date_created: 2026-07-27T12:30:23Z
date_published: 2014-09-15T00:00:00Z
date_updated: 2026-08-12T14:17:26Z
day: '15'
doi: 10.1016/j.scitotenv.2013.12.014
extern: '1'
external_id:
pmid:
- '24418218'
intvolume: ' 493'
keyword:
- Climate change
- Hydrological modeling
- Stochastic downscaling
- Uncertainty
- Water resources
- Alps
language:
- iso: eng
month: '09'
oa_version: None
page: 1171-1182
pmid: 1
publication: Science of The Total Environment
publication_identifier:
eissn:
- 1879-1026
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Does internal climate variability overwhelm climate change signals in streamflow?
The upper Po and Rhone basin case studies
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 493
year: '2014'
...
---
OA_place: publisher
OA_type: free access
_id: '22460'
abstract:
- lang: eng
text: The biological responses to precipitation within the terrestrial components
of Earth system models, or land surface models (LSMs), are mechanistically simple
and poorly constrained, leaving projections of terrestrial ecosystem functioning
and feedbacks to climate change uncertain. A number of field experiments have
been conducted or are underway to test how changing precipitation will affect
terrestrial ecosystems. Results from these experiments have the potential to vastly
improve modeled processes. However, the transformation of experimental results
into model improvements still represents a grand challenge. Here we review the
current state of precipitation manipulation experiments and the precipitation
responses of biological processes in LSMs to explore how these experiments can
help improve model realism. First, we discuss contemporary precipitation projections
and then review the structure and function of current-generation LSMs. We then
examine different experimental designs and discuss basic variables that, if measured,
would increase a field experiment's usefulness in a modeling context. Next, we
compare biological processes commonly measured in the field with their model analogs
and find that, in many cases, the way these processes are measured in the field
is not compatible with the way they are represented in LSMs, an effect that hinders
model development. We then discuss the challenge of scaling from the plot to the
globe. Finally, we provide a series of recommendations aimed to improve the connectivity
between experiments and LSMs and conclude that studies designed from the perspective
of researchers in both communities will provide the greatest benefit to the broader
global change community.
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas G.
full_name: Smith, Nicholas G.
last_name: Smith
- first_name: Vikki L.
full_name: Rodgers, Vikki L.
last_name: Rodgers
- first_name: Edward R.
full_name: Brzostek, Edward R.
last_name: Brzostek
- first_name: Andrew
full_name: Kulmatiski, Andrew
last_name: Kulmatiski
- first_name: Meghan L.
full_name: Avolio, Meghan L.
last_name: Avolio
- first_name: David L.
full_name: Hoover, David L.
last_name: Hoover
- first_name: Sally E.
full_name: Koerner, Sally E.
last_name: Koerner
- first_name: Kerstin
full_name: Grant, Kerstin
last_name: Grant
- first_name: Anke
full_name: Jentsch, Anke
last_name: Jentsch
- first_name: Simone
full_name: Fatichi, Simone
id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
last_name: Fatichi
- first_name: Dev
full_name: Niyogi, Dev
last_name: Niyogi
citation:
ama: Smith NG, Rodgers VL, Brzostek ER, et al. Toward a better integration of biological
data from precipitation manipulation experiments into Earth system models. Reviews
of Geophysics. 2014;52(3):412-434. doi:10.1002/2014rg000458
apa: Smith, N. G., Rodgers, V. L., Brzostek, E. R., Kulmatiski, A., Avolio, M. L.,
Hoover, D. L., … Niyogi, D. (2014). Toward a better integration of biological
data from precipitation manipulation experiments into Earth system models. Reviews
of Geophysics. American Geophysical Union. https://doi.org/10.1002/2014rg000458
chicago: Smith, Nicholas G., Vikki L. Rodgers, Edward R. Brzostek, Andrew Kulmatiski,
Meghan L. Avolio, David L. Hoover, Sally E. Koerner, et al. “Toward a Better Integration
of Biological Data from Precipitation Manipulation Experiments into Earth System
Models.” Reviews of Geophysics. American Geophysical Union, 2014. https://doi.org/10.1002/2014rg000458.
ieee: N. G. Smith et al., “Toward a better integration of biological data
from precipitation manipulation experiments into Earth system models,” Reviews
of Geophysics, vol. 52, no. 3. American Geophysical Union, pp. 412–434, 2014.
ista: Smith NG, Rodgers VL, Brzostek ER, Kulmatiski A, Avolio ML, Hoover DL, Koerner
SE, Grant K, Jentsch A, Fatichi S, Niyogi D. 2014. Toward a better integration
of biological data from precipitation manipulation experiments into Earth system
models. Reviews of Geophysics. 52(3), 412–434.
mla: Smith, Nicholas G., et al. “Toward a Better Integration of Biological Data
from Precipitation Manipulation Experiments into Earth System Models.” Reviews
of Geophysics, vol. 52, no. 3, American Geophysical Union, 2014, pp. 412–34,
doi:10.1002/2014rg000458.
short: N.G. Smith, V.L. Rodgers, E.R. Brzostek, A. Kulmatiski, M.L. Avolio, D.L.
Hoover, S.E. Koerner, K. Grant, A. Jentsch, S. Fatichi, D. Niyogi, Reviews of
Geophysics 52 (2014) 412–434.
das_tickbox: '1'
date_created: 2026-07-27T12:30:23Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2026-08-12T14:21:11Z
day: '01'
doi: 10.1002/2014rg000458
extern: '1'
intvolume: ' 52'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2014RG000458
month: '09'
oa: 1
oa_version: Published Version
page: 412-434
publication: Reviews of Geophysics
publication_identifier:
eissn:
- 1944-9208
issn:
- 8755-1209
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward a better integration of biological data from precipitation manipulation
experiments into Earth system models
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 52
year: '2014'
...
---
_id: '1896'
abstract:
- lang: eng
text: 'Biopolymer length regulation is a complex process that involves a large number
of biological, chemical, and physical subprocesses acting simultaneously across
multiple spatial and temporal scales. An illustrative example important for genomic
stability is the length regulation of telomeres - nucleoprotein structures at
the ends of linear chromosomes consisting of tandemly repeated DNA sequences and
a specialized set of proteins. Maintenance of telomeres is often facilitated by
the enzyme telomerase but, particularly in telomerase-free systems, the maintenance
of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms
mediated by recombination. Various linear and circular DNA structures were identified
to participate in ALT, however, dynamics of the whole process is still poorly
understood. We propose a chemical kinetics model of ALT with kinetic rates systematically
derived from the biophysics of DNA diffusion and looping. The reaction system
is reduced to a coagulation-fragmentation system by quasi-steady-state approximation.
The detailed treatment of kinetic rates yields explicit formulas for expected
size distributions of telomeres that demonstrate the key role played by the J
factor, a quantitative measure of bending of polymers. The results are in agreement
with experimental data and point out interesting phenomena: an appearance of very
long telomeric circles if the total telomere density exceeds a critical value
(excess mass) and a nonlinear response of the telomere size distributions to the
amount of telomeric DNA in the system. The results can be of general importance
for understanding dynamics of telomeres in telomerase-independent systems as this
mode of telomere maintenance is similar to the situation in tumor cells lacking
telomerase activity. Furthermore, due to its universality, the model may also
serve as a prototype of an interaction between linear and circular DNA structures
in various settings.'
acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and
K.B.).
article_number: '032701'
article_processing_charge: No
arxiv: 1
author:
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Jozef
full_name: Nosek, Jozef
last_name: Nosek
- first_name: Ľubomír
full_name: Tomáška, Ľubomír
last_name: Tomáška
citation:
ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism
of telomere length maintenance. Physical Review E. 2014;89(3). doi:10.1103/PhysRevE.89.032701
apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model
of alternative mechanism of telomere length maintenance. Physical Review E.
American Physical Society. https://doi.org/10.1103/PhysRevE.89.032701
chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical
Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review
E. American Physical Society, 2014. https://doi.org/10.1103/PhysRevE.89.032701.
ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative
mechanism of telomere length maintenance,” Physical Review E, vol. 89,
no. 3. American Physical Society, 2014.
ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative
mechanism of telomere length maintenance. Physical Review E. 89(3), 032701.
mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere
Length Maintenance.” Physical Review E, vol. 89, no. 3, 032701, American
Physical Society, 2014, doi:10.1103/PhysRevE.89.032701.
short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E 89 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2026-08-12T14:27:46Z
day: '04'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.89.032701
external_id:
arxiv:
- '1402.0430'
isi:
- '000332274100002'
intvolume: ' 89'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0430
month: '03'
oa: 1
oa_version: Submitted Version
publication: Physical Review E
publication_status: published
publisher: American Physical Society
publist_id: '5198'
scopus_import: '1'
status: public
title: Mathematical model of alternative mechanism of telomere length maintenance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '2226'
abstract:
- lang: eng
text: Coriolis force effects on shear flows are important in geophysical and astrophysical
contexts. We report a study on the linear stability and the transient energy growth
of the plane Couette flow with system rotation perpendicular to the shear direction.
External rotation causes linear instability. At small rotation rates, the onset
of linear instability scales inversely with the rotation rate and the optimal
transient growth in the linearly stable region is slightly enhanced ∼Re2. The
corresponding optimal initial perturbations are characterized by roll structures
inclined in the streamwise direction and are twisted under external rotation.
At large rotation rates, the transient growth is significantly inhibited and hence
linear stability analysis is a reliable indicator for instability.
article_number: '013001'
article_processing_charge: No
arxiv: 1
author:
- first_name: Liang
full_name: Shi, Liang
last_name: Shi
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Andreas
full_name: Tilgner, Andreas
last_name: Tilgner
citation:
ama: Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. Physical
Review E. 2014;89(1). doi:10.1103/PhysRevE.89.013001
apa: Shi, L., Hof, B., & Tilgner, A. (2014). Transient growth of Ekman-Couette
flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.89.013001
chicago: Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette
Flow.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/PhysRevE.89.013001.
ieee: L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,”
Physical Review E, vol. 89, no. 1. American Physical Society, 2014.
ista: Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical
Review E. 89(1), 013001.
mla: Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” Physical Review
E, vol. 89, no. 1, 013001, American Physical Society, 2014, doi:10.1103/PhysRevE.89.013001.
short: L. Shi, B. Hof, A. Tilgner, Physical Review E 89 (2014).
corr_author: '1'
date_created: 2018-12-11T11:56:26Z
date_published: 2014-01-06T00:00:00Z
date_updated: 2026-08-12T14:26:10Z
day: '06'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.89.013001
external_id:
arxiv:
- '1312.5095'
isi:
- '000332155800013'
intvolume: ' 89'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1312.5095
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: "Glutamaterge synaptische Ã\x9Cbertragung und Plastizität in hippocampalen
Mikroschaltkreisen"
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
publication_status: published
publisher: American Physical Society
publist_id: '4737'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transient growth of Ekman-Couette flow
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '2183'
abstract:
- lang: eng
text: 'We describe a simple adaptive network of coupled chaotic maps. The network
reaches a stationary state (frozen topology) for all values of the coupling parameter,
although the dynamics of the maps at the nodes of the network can be nontrivial.
The structure of the network shows interesting hierarchical properties and in
certain parameter regions the dynamics is polysynchronous: Nodes can be divided
in differently synchronized classes but, contrary to cluster synchronization,
nodes in the same class need not be connected to each other. These complicated
synchrony patterns have been conjectured to play roles in systems biology and
circuits. The adaptive system we study describes ways whereby this behavior can
evolve from undifferentiated nodes.'
acknowledgement: "V.B.S. is partially supported by contract MEC (Grant No. AYA2010-22111-C03-02).\r\n"
article_number: '062809'
article_processing_charge: No
arxiv: 1
author:
- first_name: Vicente
full_name: Botella Soler, Vicente
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: Paul
full_name: Glendinning, Paul
last_name: Glendinning
citation:
ama: Botella Soler V, Glendinning P. Hierarchy and polysynchrony in an adaptive
network . Physical Review E. 2014;89(6). doi:10.1103/PhysRevE.89.062809
apa: Botella Soler, V., & Glendinning, P. (2014). Hierarchy and polysynchrony
in an adaptive network . Physical Review E. American Physical Society.
https://doi.org/10.1103/PhysRevE.89.062809
chicago: Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony
in an Adaptive Network .” Physical Review E. American Physical Society,
2014. https://doi.org/10.1103/PhysRevE.89.062809.
ieee: V. Botella Soler and P. Glendinning, “Hierarchy and polysynchrony in an adaptive
network ,” Physical Review E, vol. 89, no. 6. American Physical Society,
2014.
ista: Botella Soler V, Glendinning P. 2014. Hierarchy and polysynchrony in an adaptive
network . Physical Review E. 89(6), 062809.
mla: Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony
in an Adaptive Network .” Physical Review E, vol. 89, no. 6, 062809, American
Physical Society, 2014, doi:10.1103/PhysRevE.89.062809.
short: V. Botella Soler, P. Glendinning, Physical Review E 89 (2014).
corr_author: '1'
date_created: 2018-12-11T11:56:11Z
date_published: 2014-06-16T00:00:00Z
date_updated: 2026-08-12T14:27:10Z
day: '16'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.89.062809
ec_funded: 1
external_id:
arxiv:
- '1403.3209'
isi:
- '000337733900007'
intvolume: ' 89'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1403.3209
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physical Review E
publication_status: published
publisher: American Physical Society
publist_id: '4798'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Hierarchy and polysynchrony in an adaptive network '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '1999'
abstract:
- lang: eng
text: Selection for disease control is believed to have contributed to shape the
organisation of insect societies — leading to interaction patterns that mitigate
disease transmission risk within colonies, conferring them ‘organisational immunity’.
Recent studies combining epidemiological models with social network analysis have
identified general properties of interaction networks that may hinder propagation
of infection within groups. These can be prophylactic and/or induced upon pathogen
exposure. Here we review empirical evidence for these two types of organisational
immunity in social insects and describe the individual-level behaviours that underlie
it. We highlight areas requiring further investigation, and emphasise the need
for tighter links between theory and empirical research and between individual-level
and collective-level analyses.
article_processing_charge: No
author:
- first_name: Nathalie
full_name: Stroeymeyt, Nathalie
last_name: Stroeymeyt
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social
insects. Current Opinion in Insect Science. 2014;5(1):1-15. doi:10.1016/j.cois.2014.09.001
apa: Stroeymeyt, N., Casillas Perez, B. E., & Cremer, S. (2014). Organisational
immunity in social insects. Current Opinion in Insect Science. Elsevier.
https://doi.org/10.1016/j.cois.2014.09.001
chicago: Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational
Immunity in Social Insects.” Current Opinion in Insect Science. Elsevier,
2014. https://doi.org/10.1016/j.cois.2014.09.001.
ieee: N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity
in social insects,” Current Opinion in Insect Science, vol. 5, no. 1. Elsevier,
pp. 1–15, 2014.
ista: Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in
social insects. Current Opinion in Insect Science. 5(1), 1–15.
mla: Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” Current
Opinion in Insect Science, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:10.1016/j.cois.2014.09.001.
short: N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect
Science 5 (2014) 1–15.
corr_author: '1'
date_created: 2018-12-11T11:55:08Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2026-09-03T22:30:21Z
day: '01'
department:
- _id: SyCr
doi: 10.1016/j.cois.2014.09.001
ec_funded: 1
external_id:
isi:
- '000209578900002'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 1 - 15
project:
- _id: 25DC711C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '243071'
name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society
Effects'
publication: Current Opinion in Insect Science
publication_status: published
publisher: Elsevier
publist_id: '5080'
quality_controlled: '1'
related_material:
record:
- id: '6383'
relation: dissertation_contains
- id: '6435'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Organisational immunity in social insects
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 5
year: '2014'
...
---
OA_type: free access
_id: '1980'
abstract:
- lang: eng
text: Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role
in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants
and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality
in important bacterial pathogens suggests these enzymes may represent a potential
new drug target to combat microbial pathogens. Here, we report the first crystal
structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus
thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique
dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated
C-terminal membrane-anchoring regions that are essential for membrane localization
and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with
the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding
sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure
establishes a framework for the structure-based design of small-molecule inhibitors.
acknowledgement: Funded by Health Research Council of New Zealand Royal Society
of New Zealand University of Otago New Zealand Synchrotron Group
article_processing_charge: No
article_type: original
author:
- first_name: Adam
full_name: Heikal, Adam
last_name: Heikal
- first_name: Yoshio
full_name: Nakatani, Yoshio
last_name: Nakatani
- first_name: Elyse
full_name: Dunn, Elyse
last_name: Dunn
- first_name: Marion
full_name: Weimar, Marion
last_name: Weimar
- first_name: Catherine
full_name: Day, Catherine
last_name: Day
- first_name: Edward
full_name: Baker, Edward
last_name: Baker
- first_name: Shaun
full_name: Lott, Shaun
last_name: Lott
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Gregory
full_name: Cook, Gregory
last_name: Cook
citation:
ama: 'Heikal A, Nakatani Y, Dunn E, et al. Structure of the bacterial type II NADH
dehydrogenase: a monotopic membrane protein with an essential role in energy generation.
Molecular Microbiology. 2014;91(5):950-964. doi:10.1111/mmi.12507'
apa: 'Heikal, A., Nakatani, Y., Dunn, E., Weimar, M., Day, C., Baker, E., … Cook,
G. (2014). Structure of the bacterial type II NADH dehydrogenase: a monotopic
membrane protein with an essential role in energy generation. Molecular Microbiology.
Wiley-Blackwell. https://doi.org/10.1111/mmi.12507'
chicago: 'Heikal, Adam, Yoshio Nakatani, Elyse Dunn, Marion Weimar, Catherine Day,
Edward Baker, Shaun Lott, Leonid A Sazanov, and Gregory Cook. “Structure of the
Bacterial Type II NADH Dehydrogenase: A Monotopic Membrane Protein with an Essential
Role in Energy Generation.” Molecular Microbiology. Wiley-Blackwell, 2014.
https://doi.org/10.1111/mmi.12507.'
ieee: 'A. Heikal et al., “Structure of the bacterial type II NADH dehydrogenase:
a monotopic membrane protein with an essential role in energy generation,” Molecular
Microbiology, vol. 91, no. 5. Wiley-Blackwell, pp. 950–964, 2014.'
ista: 'Heikal A, Nakatani Y, Dunn E, Weimar M, Day C, Baker E, Lott S, Sazanov LA,
Cook G. 2014. Structure of the bacterial type II NADH dehydrogenase: a monotopic
membrane protein with an essential role in energy generation. Molecular Microbiology.
91(5), 950–964.'
mla: 'Heikal, Adam, et al. “Structure of the Bacterial Type II NADH Dehydrogenase:
A Monotopic Membrane Protein with an Essential Role in Energy Generation.” Molecular
Microbiology, vol. 91, no. 5, Wiley-Blackwell, 2014, pp. 950–64, doi:10.1111/mmi.12507.'
short: A. Heikal, Y. Nakatani, E. Dunn, M. Weimar, C. Day, E. Baker, S. Lott, L.A.
Sazanov, G. Cook, Molecular Microbiology 91 (2014) 950–964.
date_created: 2018-12-11T11:55:01Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2026-09-04T11:27:46Z
day: '01'
doi: 10.1111/mmi.12507
extern: '1'
external_id:
pmid:
- '24444429'
intvolume: ' 91'
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: 950 - 964
pmid: 1
publication: Molecular Microbiology
publication_identifier:
eissn:
- 1365-2958
issn:
- 0950-382X
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5103'
status: public
title: 'Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane
protein with an essential role in energy generation'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 91
year: '2014'
...
---
OA_type: closed access
_id: '1791'
abstract:
- lang: eng
text: Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing
brain is a powerful technique to study genetic function; however, discrepancies
between knockdown and knockout murine phenotypes have left unanswered questions.
For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical
neuronal migration phenotype. Here we report that in utero electroporation of
shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx
knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target
toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts,
as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent
but not sequence-specific effect. Profiling RNAs from electroporated cells showed
a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated
the migration defect. The results suggest that shRNA-mediated knockdown can produce
untoward migration effects by altering endogenous miRNA pathways.
acknowledgement: This work was supported by the National Institutes of Health R01NS41537.
G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini
Fellowship, and A.G.F. by the Brain Behavior Research Foundation
article_processing_charge: No
article_type: original
author:
- first_name: Seungtae
full_name: Baek, Seungtae
last_name: Baek
- first_name: Géraldine
full_name: Kerjan, Géraldine
last_name: Kerjan
- first_name: Stephanie
full_name: Bielas, Stephanie
last_name: Bielas
- first_name: Jieun
full_name: Lee, Jieun
last_name: Lee
- first_name: Ali
full_name: Fenstermaker, Ali
last_name: Fenstermaker
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family
shRNA on neuronal migration associated with endogenous MicroRNA dysregulation.
Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036
apa: Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G.,
& Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal
migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2014.04.036
chicago: Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker,
Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA
on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron.
Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036.
ieee: S. Baek et al., “Off-target effect of doublecortin family shRNA on
neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.
ista: Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J.
2014. Off-target effect of doublecortin family shRNA on neuronal migration associated
with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.
mla: Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal
Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol.
82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036.
short: S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson,
Neuron 82 (2014) 1255–1262.
date_created: 2018-12-11T11:54:01Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2026-09-04T11:50:27Z
day: '18'
doi: 10.1016/j.neuron.2014.04.036
extern: '1'
external_id:
pmid:
- '24945770'
intvolume: ' 82'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 1255 - 1262
pmid: 1
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
publist_id: '5322'
status: public
title: Off-target effect of doublecortin family shRNA on neuronal migration associated
with endogenous MicroRNA dysregulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 82
year: '2014'
...
---
OA_type: closed access
_id: '1979'
abstract:
- lang: eng
text: NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme
in the respiratory chain of mitochondria and many bacteria. It couples the transfer
of two electrons between NADH and ubiquinone to the translocation of four protons
across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic
(peripheral) arm, containing all the redox centres performing electron transfer
and the membrane arm, containing proton-translocating machinery. Mitochondrial
complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic
enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently
we have determined the first atomic structure of the entire complex I, using the
enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM
helices). Structure suggests a unique coupling mechanism, with redox energy of
electron transfer driving proton translocation via long-range (up to ~200 Å) conformational
changes. It resembles a steam engine, with coupling elements (akin to coupling
rods) linking parts of this molecular machine.
article_processing_charge: No
article_type: original
author:
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Sazanov LA. The mechanism of coupling between electron transfer and proton
translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes.
2014;46(4):247-253. doi:10.1007/s10863-014-9554-z
apa: Sazanov, L. A. (2014). The mechanism of coupling between electron transfer
and proton translocation in respiratory complex I. Journal of Bioenergetics
and Biomembranes. Springer Nature. https://doi.org/10.1007/s10863-014-9554-z
chicago: Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer
and Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics
and Biomembranes. Springer Nature, 2014. https://doi.org/10.1007/s10863-014-9554-z.
ieee: L. A. Sazanov, “The mechanism of coupling between electron transfer and proton
translocation in respiratory complex I,” Journal of Bioenergetics and Biomembranes,
vol. 46, no. 4. Springer Nature, pp. 247–253, 2014.
ista: Sazanov LA. 2014. The mechanism of coupling between electron transfer and
proton translocation in respiratory complex I. Journal of Bioenergetics and Biomembranes.
46(4), 247–253.
mla: Sazanov, Leonid A. “The Mechanism of Coupling between Electron Transfer and
Proton Translocation in Respiratory Complex I.” Journal of Bioenergetics and
Biomembranes, vol. 46, no. 4, Springer Nature, 2014, pp. 247–53, doi:10.1007/s10863-014-9554-z.
short: L.A. Sazanov, Journal of Bioenergetics and Biomembranes 46 (2014) 247–253.
date_created: 2018-12-11T11:55:01Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2026-09-04T11:48:14Z
day: '01'
doi: 10.1007/s10863-014-9554-z
extern: '1'
external_id:
pmid:
- '24943718'
intvolume: ' 46'
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 247 - 253
pmid: 1
publication: Journal of Bioenergetics and Biomembranes
publication_identifier:
eissn:
- 1573-6881
issn:
- 0145-479X
publication_status: published
publisher: Springer Nature
publist_id: '5104'
status: public
title: The mechanism of coupling between electron transfer and proton translocation
in respiratory complex I
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 46
year: '2014'
...
---
OA_place: repository
OA_type: green
_id: '1761'
abstract:
- lang: eng
text: Metal silicides formed by means of thermal annealing processes are employed
as contact materials in microelectronics. Control of the structure of silicide/silicon
interfaces becomes a critical issue when the characteristic size of the device
is reduced below a few tens of nanometers. Here, we report on silicide clustering
occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This
phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling
spectroscopy. Our results provide evidence for the segregation of a PtSi cluster
with a diameter of a few nanometers from the silicide contact. The cluster acts
as a metallic quantum dot giving rise to distinct signatures of quantum transport
through its discrete energy states.
acknowledgement: This work was supported by the Agence Nationale de la Recherche and
by the EU through the ERC Starting Grant HybridNano
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Massimo
full_name: Mongillo, Massimo
last_name: Mongillo
- first_name: Panayotis
full_name: Spathis, Panayotis
last_name: Spathis
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
- first_name: Pascal
full_name: Gentile, Pascal
last_name: Gentile
- first_name: Riccardo
full_name: Rurali, Riccardo
last_name: Rurali
- first_name: Xavier
full_name: Cartoixà, Xavier
last_name: Cartoixà
citation:
ama: Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed
by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025
apa: Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali,
R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport
spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025
chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi,
Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon
Probed by Transport Spectroscopy.” Physical Review X. American Physical
Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025.
ieee: M. Mongillo et al., “PtSi clustering in silicon probed by transport
spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society,
2014.
ista: Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà
X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical
Review X. 3(4).
mla: Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.”
Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025.
short: M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali,
X. Cartoixà, Physical Review X 3 (2014).
date_created: 2018-12-11T11:53:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2026-09-04T11:52:28Z
day: '01'
doi: 10.1103/PhysRevX.3.041025
extern: '1'
external_id:
arxiv:
- abs/1407.5413
intvolume: ' 3'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.5413
month: '01'
oa: 1
oa_version: None
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
publist_id: '5363'
status: public
title: PtSi clustering in silicon probed by transport spectroscopy
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 3
year: '2014'
...
---
OA_type: closed access
_id: '1312'
abstract:
- lang: eng
text: We derive upper bounds on the waiting time of solutions to the thin-film equation
in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient
conditions on the initial data for instantaneous forward motion of the free boundary.
For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a
logarithmic correction term. Note that the case n = 2 corresponds-with a grain
of salt-to the assumption of the Navier slip condition at the fluid-solid interface.
We also obtain results in the regime of strong slippage n ∈ (1,2); however, in
this regime we expect them not to be optimal. Our method is based on weighted
backward entropy estimates, Hardy's inequality and singular weight functions;
we deduce a differential inequality which would enforce blowup of the weighted
entropy if the contact line were to remain stationary for too long.
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: 'Fischer JL. Upper bounds on waiting times for the Thin-film equation: The
case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818.
doi:10.1007/s00205-013-0690-0'
apa: 'Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage. Archive for Rational Mechanics and Analysis.
Springer Nature. https://doi.org/10.1007/s00205-013-0690-0'
chicago: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation:
The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis.
Springer Nature, 2014. https://doi.org/10.1007/s00205-013-0690-0.'
ieee: 'J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage,” Archive for Rational Mechanics and Analysis,
vol. 211, no. 3. Springer Nature, pp. 771–818, 2014.'
ista: 'Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3),
771–818.'
mla: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation:
The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis,
vol. 211, no. 3, Springer Nature, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.'
short: J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818.
date_created: 2018-12-11T11:51:18Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2026-09-04T11:54:26Z
day: '01'
doi: 10.1007/s00205-013-0690-0
extern: '1'
intvolume: ' 211'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 771 - 818
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
publist_id: '5959'
status: public
title: 'Upper bounds on waiting times for the Thin-film equation: The case of weak
slippage'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 211
year: '2014'
...
---
OA_type: closed access
_id: '1309'
abstract:
- lang: eng
text: We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation
display infinite speed of support propagation. We apply our method to the case
of the quantum drift-diffusion equation which augments the DLSS equation with
a drift term and possibly a second-order diffusion term. The proof is accomplished
using weighted entropy estimates, Hardy's inequality and a family of singular
weight functions to derive a differential inequality; the differential inequality
shows exponential growth of the weighted entropy, with the growth constant blowing
up very fast as the singularity of the weight becomes sharper. To the best of
our knowledge, this is the first example of a nonnegativity-preserving higher-order
parabolic equation displaying infinite speed of support propagation.
article_processing_charge: No
article_type: original
author:
- first_name: Julian L
full_name: Fischer, Julian L
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0
apa: Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0
chicago: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations
and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0.
ieee: J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models,” Nonlinear Differential Equations
and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014.
ista: Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. 21(1), 27–50.
mla: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations
and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0.
short: J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014)
27–50.
date_created: 2018-12-11T11:51:17Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2026-09-04T11:56:53Z
day: '01'
doi: 10.1007/s00030-013-0235-0
extern: '1'
intvolume: ' 21'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 27 - 50
publication: Nonlinear Differential Equations and Applications
publication_identifier:
eissn:
- 1420-9004
issn:
- 1021-9722
publication_status: published
publisher: Birkhäuser
publist_id: '5960'
status: public
title: Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 21
year: '2014'
...
---
OA_type: closed access
_id: '1058'
abstract:
- lang: eng
text: Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy)
methods typically rely on transiently transferring fluorophores between two states,
whereby this transfer is usually laid out as a switch. However, depending on whether
this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted)
or stochastically on a single-molecule basis, specific requirements on the fluorophores
are imposed. Therefore, the fluorophores are usually utilized just for one class
of methods only. In this study we demonstrate that the reversibly switchable fluorescent
protein Dreiklang enables live-cell recordings in both spatially controlled and
stochastic modes. We show that the Dreiklang chromophore entails three different
light-induced switching mechanisms, namely a reversible photochemical one, off-switching
by stimulated emission, and a reversible transfer to a long-lived dark state from
the S1 state, all of which can be utilized to overcome the diffraction barrier.
We also find that for the single-molecule- based stochastic GSDIM approach (ground-state
depletion followed by individual molecule return), Dreiklang provides a larger
number of on-off localization events as compared to its progenitor Citrine. Altogether,
Dreiklang is a versatile probe for essentially all popular forms of live-cell
fluorescence nanoscopy.
article_processing_charge: No
article_type: original
author:
- first_name: Nickels
full_name: Jensen, Nickels
last_name: Jensen
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Katrin
full_name: Willig, Katrin
last_name: Willig
- first_name: Flavie
full_name: Lavoie Cardinal, Flavie
last_name: Lavoie Cardinal
- first_name: Tanja
full_name: Brakemann, Tanja
last_name: Brakemann
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
citation:
ama: Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic
super-resolution microscopy with the reversibly switchable fluorescent protein
dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034
apa: Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell,
S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem.
Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034
chicago: Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal,
Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic
Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein
Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.
ieee: N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem,
vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.
ista: Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs
S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy
with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4),
756–762.
mla: Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution
Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem,
vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034.
short: N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell,
S. Jakobs, ChemPhysChem 15 (2014) 756–762.
date_created: 2018-12-11T11:49:55Z
date_published: 2014-03-17T00:00:00Z
date_updated: 2026-09-04T12:18:04Z
day: '17'
doi: 10.1002/cphc.201301034
extern: '1'
external_id:
pmid:
- '24497300'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 756 - 762
pmid: 1
publication: ChemPhysChem
publication_identifier:
eissn:
- 1439-7641
issn:
- 1439-4235
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6332'
status: public
title: Coordinate-targeted and coordinate-stochastic super-resolution microscopy with
the reversibly switchable fluorescent protein dreiklang
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2014'
...
---
_id: '10895'
abstract:
- lang: eng
text: 'Due to their sessile lifestyles, plants need to deal with the limitations
and stresses imposed by the changing environment. Plants cope with these by a
remarkable developmental flexibility, which is embedded in their strategy to survive.
Plants can adjust their size, shape and number of organs, bend according to gravity
and light, and regenerate tissues that were damaged, utilizing a coordinating,
intercellular signal, the plant hormone, auxin. Another versatile signal is the
cation, Ca2+, which is a crucial second messenger for many rapid cellular processes
during responses to a wide range of endogenous and environmental signals, such
as hormones, light, drought stress and others. Auxin is a good candidate for one
of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling
is poorly understood. Here, we will provide an overview of possible developmental
and physiological roles, as well as mechanisms underlying the interconnection
of Ca2+ and auxin signaling. '
article_processing_charge: No
article_type: original
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants.
2013;2(4):650-675. doi:10.3390/plants2040650'
apa: 'Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action.
Plants. MDPI. https://doi.org/10.3390/plants2040650'
chicago: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin
Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.'
ieee: 'S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants,
vol. 2, no. 4. MDPI, pp. 650–675, 2013.'
ista: 'Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants.
2(4), 650–675.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.”
Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.'
short: S. Vanneste, J. Friml, Plants 2 (2013) 650–675.
corr_author: '1'
date_created: 2022-03-21T07:13:49Z
date_published: 2013-10-21T00:00:00Z
date_updated: 2024-10-09T21:01:52Z
day: '21'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3390/plants2040650
external_id:
pmid:
- '27137397'
file:
- access_level: open_access
checksum: fb4ff2e820e344e253c9197544610be6
content_type: application/pdf
creator: dernst
date_created: 2022-03-21T12:12:56Z
date_updated: 2022-03-21T12:12:56Z
file_id: '10916'
file_name: 2013_Plants_Vanneste.pdf
file_size: 670188
relation: main_file
success: 1
file_date_updated: 2022-03-21T12:12:56Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
keyword:
- Plant Science
- Ecology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 650-675
pmid: 1
publication: Plants
publication_identifier:
issn:
- 2223-7747
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calcium: The missing link in auxin action'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2013'
...
---
_id: '10897'
abstract:
- lang: eng
text: Taking images is an efficient way to collect data about the physical world.
It can be done fast and in exquisite detail. By definition, image processing is
the field that concerns itself with the computation aimed at harnessing the information
contained in images [10]. This talk is concerned with topological information.
Our main thesis is that persistent homology [5] is a useful method to quantify
and summarize topological information, building a bridge that connects algebraic
topology with applications. We provide supporting evidence for this thesis by
touching upon four technical developments in the overlap between persistent homology
and image processing.
acknowledgement: This research is partially supported by the European Science Foundation
(ESF) under the Research Network Programme, the European Union under the Toposys
Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Persistent homology in image processing. In: Graph-Based
Representations in Pattern Recognition. Vol 7877. LNCS. Berlin, Heidelberg:
Springer Nature; 2013:182-183. doi:10.1007/978-3-642-38221-5_19'
apa: 'Edelsbrunner, H. (2013). Persistent homology in image processing. In Graph-Based
Representations in Pattern Recognition (Vol. 7877, pp. 182–183). Berlin, Heidelberg:
Springer Nature. https://doi.org/10.1007/978-3-642-38221-5_19'
chicago: 'Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In Graph-Based
Representations in Pattern Recognition, 7877:182–83. LNCS. Berlin, Heidelberg:
Springer Nature, 2013. https://doi.org/10.1007/978-3-642-38221-5_19.'
ieee: H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based
Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877,
pp. 182–183.
ista: 'Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based
Representations in Pattern Recognition. GbRPR: Graph-based Representations in
Pattern RecognitionLNCS vol. 7877, 182–183.'
mla: Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” Graph-Based
Representations in Pattern Recognition, vol. 7877, Springer Nature, 2013,
pp. 182–83, doi:10.1007/978-3-642-38221-5_19.
short: H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition,
Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.
conference:
end_date: 2013-05-17
location: Vienna, Austria
name: 'GbRPR: Graph-based Representations in Pattern Recognition'
start_date: 2013-05-15
corr_author: '1'
date_created: 2022-03-21T07:30:33Z
date_published: 2013-06-01T00:00:00Z
date_updated: 2025-04-15T08:37:54Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-38221-5_19
ec_funded: 1
intvolume: ' 7877'
language:
- iso: eng
month: '06'
oa_version: None
page: 182-183
place: Berlin, Heidelberg
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Graph-Based Representations in Pattern Recognition
publication_identifier:
eisbn:
- '9783642382215'
eissn:
- 1611-3349
isbn:
- '9783642382208'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Persistent homology in image processing
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7877
year: '2013'
...